One way to do this is to define a reasonable model using differential equations based on what you know about the drug and the metabolite. E.g., a one compartmental model for the parent and possibly interconversion of parent to metabolite (does metabolism occur in central compartment, is metabolism reversible?, does the metabolite also follow one compartment dispostion?) One then needs to define a CMT data item to specify which compartment the observation corresponds to (central for the parent, some other for the metabolite based on the metabolite portion of the structural model you are proposing.)

> Be careful I believe that this model may have identifiability problems. As
> it is written, CL (parent drug clearance should refer to clearance of all
> parent drug elimination routes except this particular metabolic route (it
> is accounted for by KF in the equation). In addition I don't think VMT is
> identifiable (as CLM) unless you know the fraction of parent drug
> converted to this particular metabolite (a problem similar for parent drug
> CL and VP in case of an oral drug, you need to know F, the absolute
> bioavailability).
>
An alternative code is this one (using ADVAN 6). The parent has 3 compartment IV route and the metabolite 2 compartments (compt 4 and 5) :

K=CL/V ; K elimination for parent, all routes
S1=V ; Scaling for parent
S4=1 ; Scaling for the metabolite, should be V4 but it is unidentifiable since we don't know the fraction of parent CL accounted for by this metabolic route

The code originally given mostly likely DOES HAVE IDENTIFIABILITY PROBLEMS (see caveat added). However, its intent was mainly didactic -> how to code a parent-metabolite. The details, of course, are dependent on the usual modeling constraints: does it reflect what we know about the drug?, is it "reasonable"?, does the data we have allow identification of defined parameters?, etc. Also, choice of ADVAN 6, 8 or 9 is, in the end, what works for your data and model.